I only have a few things that I want to see in the game (short-term, mid-term, long-term)

first and foremost, I am a captain of a star ship, I have a crew that I give orders to and they comply to the beat of there ability
what I am saying is I want to give orders and not do everything myself, (security officer) options should be fire at will, meaning he picks his own targets and fires at what and when he wants,concentrate fire, meaning fire only on selected target.
(helmsmen) options should be, follow target, orbit target, keep at distance, face target,exc, the other officers I cant think of auto actions for them.

1: more costume choices in both tailor and c-store
2: open roaming of personal ship, perhaps with a conference room for fleet meetings.
3: larger galaxy, that would take an entire day of playing to reach one end to the other.
4: planet colonizing, terraform, (genesis)
5: end game stuff (don't let me get Bord)

Fixing the exchange so that it is sortable beyond just typing in a name
Fix auto entering enemy fights in the sectors
Memory alpha revamp-This needs to be just completely revamped but say with our own crafting stations so it is totally random when you unlock other scientists.
There should be more than 4 or 5 ranks in reality there should be many so people actually feel they are achieving something.
Get rid of the skill cap.
Make training your points at the begining of a new level not everytime you get a few points.
Space maps should be much much larger we have to remember this is space and we need time to travel places then you have room for other stuff within the maps
Make ships so that you can target a specific part of the ship like an engine, gun, cannon, shield and disable it

Mid-term requests

More high level content but with both the option of doing solo and with a group Lord of the rings online does this.
Make space flying more realistic instead of spiraling up and down.
More ship selection
Make planet maps larger with more to do on them.

Long-term requests

Make ships like a second home so that you can walk around the ships and use them for storage. Good example is Star Wars Galaxies ships
Make achievements a big deal add titles for achieving things like killing so many klingons or killing so many of one type of species. This can go above and beyond just killing stuff but there should be a page just for that.
Add Crafting to the game through memory alpha as above.
Randomly put a new species or planet within the game without notice so that there can be firsts and people actually feel they did discover something.

More options to sort the Exchange. Like by price and sub categories.
Better ship controls.. please let me fly straight up or straight down.
More life and more civilizations on alien planets.. if I'm going to have to scan 5 objects on a planet, at least make it exciting with some dangrous or interesting floura or fauna. Let there be a chance to stumble on something interesting like special loot or a mission that takes you into a cave...

Mid term:
More ships/classes. Can we have something between an escort and a cruiser like a destroyer? And somethign between Science and Cruiser like Frigates? Call them hybrids.

Long Term:
Content!!!!
I'd also love episodes that take place on my own ship. Holodeck accidents, repeling boarders that came on while discovering an alien world on a charting mission, solving a "who done it", etc. You have thousands of episodes of stories to harvest from, you don't even have to get that creative.

So far most of the requests I do have are already addressed..in no real order:

Primary:
1: Better ship designs, Those varaints in the Exploratory Cruiser section are not appealing (I'd intiate self destruct just to put the ship out of its misery). Also the pylons on the Sovereign Class are not curved, a bit trivial but it is a bit irritating to look at. The models designed for Bridge Commander were really accurate and even used for a mod for Galactic Civilizations 2.
2: Allow customization of personal equipment. Make it to where an engineer has to reach a certain skill level or rank to be able to modify equipment. If we can customize the ship, why not our ground gear.
3: More diplomatic missions with REAL choices to make and ramifications for those choices. Actually, more missions in general.

Secondary:
1: Option for an Admiral style uniform. A tunic instead of the traditional shirt.
2: 360 rotation for the ship instead of the spiral turn in order to reach enemies/objectives below or above you.
3: (If possible)Functional Bridge/Ship interiors.

Overall Im happy with the game. Its still early and I know Cryptic's primary concern will be bug hunting for the next few months. Once STO gets stable on its feet, I can't wait for the natural evolution of this game that will put a smile on everyone's face. That way we can get the bad taste of JJ Abram's movie out of our mouth's.

Short-Term:
Provide an icon for every single effect, especially those with a random chance, and include the time to expire. If I'm healing I would like to be able to see when a teammate got viraled and I'd like to see just how often my plasma beams inflict the DoT
Allow ship-switching and mail at every main starbase. I'd rather not have to burn a transwarp every time I want to send a friend a new weapon.

Mid-Term:
Prevent Kamikaze attacks from being a primary attack option. Those skills should only be used in desperate situations, more desperate than just getting killed.
Make Memory Alpha viable in some way. I don't have any concrete suggestions, but I consider MA a waste of time and inventory space at this point.
More variety in PvP. You've made it a huge part of the game yet you've created so little content for it.
Introduce a hard mode.

Long-Term:
More variety of missions. I'd like to be able to level up without feeling like I'm forced to complete every mission that is presented to me.
Meaningful PvP, areas that allow open PvP with a flagging system
Instances that have more to do in them than whatever the current mission is. Allow large areas where players have a number of possible things to do, where they can fly around and see other players doing other things, and where you would have to be aware of the other faction's players being there but you would go there primarily for PvE. Borg Hunt is close but it's not enough.

Short Term
- Fix away team AI. My officers always jump INTO fire and OFF cliffs (usually into lava when they can). Or can't figure out how to walk through a doorway.
- No More Rubberband engines. It's tiring having to cross a sector 3 times just to get to the other side (sounds like a bad "Why did the chicken cross the road 3 times?" joke, my guess to an answer would be "Because he played too much STO"!)
- More Captain/Admiral Content. Many people are aready at or very near endgame, myself included, and I have to spend several hours each level grinding explores and defense because there aren't enough story missions. Which is really pointless in the end because there isnt anything to do once you reach admiral.
- 360 degree space. I know it is posted everywhere, but it's everywhere because people want it.

Mid Term
- Endgame Content. I know you may think I posted this already but no, my earlier point was about content between Commander and Admiral. This one is about wanting something to do with my friends AT Admiral. Besides grinding gear and BOff Points.
- Repecs. Need I say more? Ok, I will. At admiral I hate being stuck with countless skills I can't use. I know it's being worked on but I'd still like to see it sooner rather than later.
- Choices/Reputations. I know these are extremely difficult to work into a game so I won't hold my breath. Some examples would be the escort mission in romulan space where you murder all the scientists because the Ambassador is an Udine in disguise. I figured that out 5 minutes in a spent the whole mission wishing I could kill her instead of murdering the scientists but I couldn't. Another thing would be a Section 31 Arc; We already do a mission to chose between Starfleet or Section 31. Why not have it carry over; if you chose section 31 you get missions from section 31 to further one of their agendae. If you chose starfleet you come across missions to stop a section 31 plot.

Long Term
- More areas. I know these are coming as expansions in the future but it doesn't change the fact that I want to see them. I would love to go explore the Delta or Gamma Quadrants.
- Story. Right now the game contains 3 very seperate and rudimentary story arcs. None of which give the sense that the Federation is in any sort of trouble. The "Klingong Invasions/War" seems to be limited to the feds invading klingon space. The romulans are developing ultimate war ships that I went face to face with in a low level science ship and blew them out of the sky, not to mention having destroyed several research facilities and half of their fleet single handedly. As for the Cardassians, they have me hunting down terrorist cells an apparently all cardassians are part of this terrorist minority. It would be really nice if the story could make these factions really threatening and scary, even try to tie the war together so I don't feel like I'm moving between different games every time I go to a different sector.
- Levels/Skill points/Rank. I don't care that there IS a Skill Point Cap but It's too easy and too fast to reach skill point cap. Why can I reach Admiral in just over a week, and where do I go from there? Theres nothing beyond admiral in Star Fleet. Even with expansions in story and new zones what is the point? I can't go past admiral, I can't get a new ship or more abilities. I guess my main point here is that in the long term I'd like to SEE a long term, as it stand right now I might get 6-8 weeks of play out of the game to get an admiral of each class and a max Klingon, then just log in for a few days to play out each expansion (if ithe expansions are worth the cost) and then shelve the game again for a few months.

Either put away the skill cap or rework the skill system to work well with a cap.
More choices in missions, like one way combat the other one diplomatic or something.
Make cruiser a bit more comfortable to fly, either by giving them a kind of "loot-trector-beam" or increase the range for loot to be collected.
More costume,ehrm, I mean, uniform options.
Skirts for the TOS uniform!
More and better communication from the devs, for example what is planned according the skill cap, remove it when the content for level 50 is in (like in CoH where it was some weeks after release that you could level to 50)